I did one of those about 6 years ago so the memory's a little fuzzy. I had both complete vehicles to work with and swapped everything that was different. It's a lot. If I didn't have both complete bodies sitting there it would have really sucked to do. Swap the fuel lines first as it's hard to get them in with the engine there! The motor mount pads that bolt to the unibody are different. I don't remember exactly on the crossmember but I think there's two sets of bolt holes and it fit on one or the other.
Everywhere something needs to bolt up there'll already be a dimple, just drill it out- for the cooling bottle bracket and stuff like that.
Go to the junkyard and buy a 4.0 xj for all the small stuff. It'll be worth the money just in fuel lines alone, not to mention wire harnesses, radiator supports etc. When mine was finished I took it to the state smog shop and he didn't believe it wasn't factory. It was- just not on that vehicle.